My guess is that one of the pins in the connectors under the hood is not making contact. Look into the connectors and see if anything looks displaced. If so, straighten it out and it will probably work fine.
You are mostly correct. One thing that you are wrong on is that you can shut off your engine any time you would like to, even during a regen cycle. The time it takes to do a regen is about 20 minutes and you should be traveling at least 30 MPH. If you do not meet these guidelines, it will...